As far as I understand, Syncthing should just update the mtime if the contents are identical.
Edit: The information below is incorrect. For why, read the follow-up posts.
If you use File Versioning though, then yes, the existing files will be moved there (even if they only differ by mtime). Is this what is happening on your side?
If yes, then this is likely the intended behaviour, and for a good reason. For example, If I open a 20-year-old Word document and by mistake click “save”, its mtime will be updated despite making no changes to its contents. In such a case, I will then go and restore the previous “version” from .stversions (because, at least for myself, the mtime conveys a very important message here, i.e. that this is a very old file and not something created just today).